1
ELECTRONIC SUPPLEMENTARY MATERIAL
Appendix 1. Details of all localities sampled, with geographic coordinates, the D-loop haplotypes detected (see appendix 2) and the numbers of
individuals scored for nuclear markers, tail:body length ratio, skull morphology and coat colour (see appendix 3). The grand total was 755 mice
(277 fresh carcasses collected on the New Zealand mainland 1999 - 2000; 29 carcases collected on the outlying islands 2000 - 2006; and 449
archived skulls with associated carcass data, collected 1973 - 1987), but most analyses used only subsamples of a given collection. The localities
are shown in order of latitude (with most northerly first). All localities are mapped in figure 1. The number codes (1 – 17) and letter codes (A –
H) relate to localities that have provided molecular and morphological data, respectively. *Collections described by King (1982) and King et al.
(1996); **collections described by Efford et al. (1988).
Locality
Key
Lat °
Long ° E
D-loop
D-loop
D11 cenB2
Btk
Abpa
Zfy2
TBLR/skull Coat colour
(figure 1)
S
or ° W
haplotypes
n
n
n
n
n
n
n
Bay of Islands 1
35°20'
174°10' E
domNZ.4
6
6
6
6
3
-
11
Ruatangata
37°00'
175°00' E
domNZ.4 (1)
5
5
3
5
2
-
5
2
domNZ.9 (3)
domNZ.10 (1)
Waikato
3
37°50'
175°20' E
domNZ.4
21
12
12
10
4
-
31
Pureora*
A
38°30'
175°40' E
-
-
-
-
-
-
218
-
2
Napier
4
39°30'
176°50' E
domNZ.1 (5)
6
3
3
2
2
-
13
4
1
1
1
-
-
15
domNZ.3 (1)
Taranaki
5
39°30'
174°20' E
domNZ.4 (2)
domNZ.6 (2)
Mana I. **
B
41°00'
174°40' E
-
-
-
-
-
-
117
-
Wellington
6
41°20'
174°40' E
casNZ.1 (7)
9
6
6
3
4
-
18
(Karori)
musNZ.1 (2)
Nelson Lakes
7, C
41°50'
172°50' E
domNZ.4
9
6
6
6
1
14
53
Craigieburn*
D
43°10'
171°40' E
-
-
-
-
-
-
36
-
Ashburton
8
43°50'
171°50' E
domNZ.1 (1)
4
4
4
4
2
-
4
domNZ.4 (1)
domNZ.9 (2)
Eglinton*
E
44°50'
168°00' E
-
-
-
-
-
-
42
-
Hollyford*
F
44°50'
168°10' E
-
-
-
-
-
-
36
-
Dunedin
9
45°50'
170°40' E
casNZ.1
4
3
3
3
1
-
4
10, G
45°50'
167°30' E
casNZ.1
3
3
3
3
1
59
73
(Taiaroa)
Borland
3
Grebe
11, H
45°50'
167°20' E
casNZ.1
3
3
3
3
2
27
43
S Fiordland
12
46°10'
167°40' E
casNZ.1 (2)
3
3
3
3
3
-
7
casNZ.3 (1)
Outlying
islands
Chatham I.
13
43°50'
176°30' W casNZ.2
2
-
-
-
-
-
-
Pitt I.
14
44°20'
176°10' W domNZ.7
5
-
-
-
-
-
-
Antipodes I.
15
49°40'
178°50' E
domNZ.8
6
-
-
-
-
-
-
Auckland I.
16
50°43'
166°20' E
domNZ.4 (5)
6
-
-
-
-
-
-
10
-
-
-
-
-
-
106
55
53
49
25
549
277
domNZ.5 (1)
Macquarie I.
17
54°40'
158°50' E
domNZ.1 (9)
domNZ.2 (1)
Totals
REFERENCES
Efford, M. G., Karl, B. J. & Moller, H. 1988 Population ecology of Mus musculus on Mana Island, New Zealand. J. Zool. 216, 539-563.
4
King, C. M. 1982 Age structure reproduction in feral New Zealand populations of the house mouse (Mus musculus), in relation to seedfall of southern beech. N. Z. J.
Zool. 9, 467-479.
King, C. M., Innes, J. G., Flux, M. & Kimberley, M. O. 1996 Population biology of small mammals in Pureora Forest Park: 2. The feral house mouse (Mus musculus).
N. Z. J. Ecol. 20, 253-269.
5
Appendix 2. D-loop haplotypes found in house mice from New Zealand, including sequences
characteristic of the subspecies Mus musculus domesticus (A), M. m. musculus (B) and M. m.
castaneus (C). Nucleotide substitutions and indels are shown with reference to the numbering
system of Bibb et al. (1981), based on a M. m. domesticus-type sequence. A dot indicates identity to
this sequence. Each insertion or deletion relative to the sequence of Bibb et al. is indicated by an ‘i’
or a ‘d’, respectively. For a deletion, a dash is shown in the sequence concerned at the relevant
nucleotide position. For an insertion, a dash is shown in the Bibb et al. sequence; the insertion
occurs after the nucleotide position indicated. A 3-bp insertion of CTC for domNZ.7 is indicated
with a ‘+’. The insertion of Cs after position 160087 for M. m. domesticus, and after position
160094 for M. m. castaneus add to a string of Cs and are positioned arbitrarily. Also included are
representative published musculus and castaneus sequences (GenBank: U47498, U47534; Prager et
al. 1996). Note that Bayona-Bafaluy et al. (2003) consider that the Bibb et al. (1981) sequence had
some errors and that there was an incorrectly inserted T at site 15823, an incorrect A at site 16119
where there should have been a C, and at site 16240 (or 16241 as shown here) there was an
incorrectly inserted A.
6
A
1
1
5
6
4555555555555556899000122222
9223444556778893212178145678
3690159019232877325287910803
dd
d
ii d
Bibb et al.
TTTCAAATATACCTCTTCCA--AAGTCT
domNZ.1
................-.....C-....
domNZ.2
.......--.......-.....C-....
domNZ.3
...........T....-.....C-....
domNZ.4
...A...--.......-.....C-....
domNZ.5
...A...--.......-....CC-....
domNZ.6
A....G.......CT.-TT..CC-.C..
domNZ.7
A......--....CT.-TT.+.C-.CTC
domNZ.8
AC.....--CT...TC-T.C..C-.C..
domNZ.9
A.CTG..--...T.T.-T....C-AC..
domNZ.10
A.CTG.C--...T.T.-T....C-AC..
B
1
1
5
6
333444555555555555555555555556890111222222
699149011112344445556677788993219147014468
345713213486023480127823828047324999681487
dd
d
d i
d
Bibb et al.
GTAACTAGTCTTCTCATTATCTACTCTAGTTC-AAATCATTC
U47498 (type 1)
ACATTATAATCCTCTGC--AAC-TCTCTAT-TACTGCC-CCT
musNZ.1
ACGTTATAATCCTCTGC--AAC-TCTCTAC-TACTGCT-CCT
7
C
1
1
5
6
34444455555555555555555555589000011122222
63444911122344455556667778921469901404446
31139313446023401247893582032494489961488
dd
d
ii
d
Bibb et al.
GCCGTTGTCATCTCATATCCTTCCTCATCGC--AAATATGT
U47534 (type 1)
ATTGCAAATGCTCTG--CCACCTCCTT-TTTA.GCTC-CGC
casNZ.1
ATTACAAATGCTCTG--CTACCTCCTT-TTTA.GCTC-CGC
casNZ.2
ATTGCAAATACTCTG--CCACCTTCTT-TTTACGCTC-CAC
casNZ.3
ATTACAAATACTCTG--CTACCTCCTT-TTTA.GCTC-CGC
REFERENCES
Bayona-Bafaluy, M. P., Acín-Pérez. R., Mullikin, J. C., Park, J. S., Moreno-Loshuertos, R., Hu, P.,
Pérez-Martos, A., Fernández-Silva, P., Bai, Y. & Enríquez, J. A. 2003 Revisiting the mouse
mitochondrial DNA sequence. Nucleic Acids Res. 31, 5349-5355.
Bibb, M. J., Van Etten, R. A., Wright, C. T., Walberg, M. W. & Clayton, D. A. 1981 Sequence and
gene organization of mouse mitochondrial DNA. Cell 26, 167-180.
Prager, E. M., Tichy, H. & Sage, R. D. 1996 Mitochondrial DNA sequence variation in the eastern
house mouse, Mus musculus: comparison with other house mice and report of a 75-bp
repeat. Genetics 143, 427-446.
8
Appendix 3. Distribution of back and belly colours of 277 mice collected in New Zealand 1999 2000 (Jamieson 2001). Colours defined from standard Munsell soil colour charts.
total
back colour
brown/
dark
brown
belly colour
black
black
brown
brown
14
brown grey
1
creamy brown
10
3
grey
14
6
grey brown
6
8
grey tan
2
pale brown
6
pale grey
light
brown
brown
1
15
1
13
3
2
1
26
14
2
1
157
164
1
1
tan
33
3
white
3
1
1
total
grey
dark grey grey
89
1
179
1
37
4
3
2
1
1
277
REFERENCES
Jamieson, P. 2001 The taxonomic identification of the New Zealand house mouse. MSc thesis,
University of Waikato, Hamilton.
9
Appendix 4. The detailed phylogenetic tree for Mus musculus musculus and M. m. castaneus after
Bayesian analysis, as summarized in figure 2B in the paper. All posterior probabilities of 0.60 or
greater are shown for branches leading to New Zealand haplotypes. These haplotypes are as listed
in Appendices 1 and 2 and are highlighted in grey; for other haplotypes, the GenBank number is
given. Countries of occurrence of each haplotype are listed as follows: AT, Austria; CZ, Czech
Republic; DE, Germany; GE, Georgia; HR, Croatia; IR, Iran; JP, Japan; KR, South Korea; KZ,
Kazakhstan; MD, Moldova; NZ, New Zealand; PK, Pakistan; PL, Poland; RS, Serbia; RU, Russia;
SK, Slovakia; TH, Thailand; TM, Turkmenistan; UA, Ukraine.